Align ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)
to candidate WP_084934993.1 HA51_RS13475 sugar ABC transporter ATP-binding protein
Query= uniprot:D8J1T6 (255 letters) >NCBI__GCF_002095475.1:WP_084934993.1 Length = 500 Score = 140 bits (354), Expect = 4e-38 Identities = 79/228 (34%), Positives = 132/228 (57%), Gaps = 14/228 (6%) Query: 5 LLKIRDVSKRFGGLQALNGVGITIERGQIYGLIGPNGAGKTTFFNVITGLYQPDTGTFEL 64 LL++R +SKRFG ++AL V +T++ G+I+ L G NGAGK+T N+I G+ +PD+G L Sbjct: 4 LLELRGISKRFGAVKALQEVDLTLQAGEIHALAGENGAGKSTLMNIIDGILRPDSGEIWL 63 Query: 65 DGKPYSPSAPHEVAKAGIARTFQNIRLFGEMTVLENVMVGCHVRTKQNVFGAVFRHKAAR 124 DGKP + +P E + GI Q I L ++++ EN+ + R G + HK Sbjct: 64 DGKPVTIRSPREAQQLGIGLVHQEIALCPDISIYENIWMAHQQR------GLLLPHK--- 114 Query: 125 EEEAAIREKSQKLLDFVGIGQFAKRTARHLSYGDQRRLEIARALATDPQLLALDEPAAGM 184 A+RE++Q++++ + +K+ LS Q+ +EIA+AL D +LL LDEP A + Sbjct: 115 ----ALRERAQQVMNRLAPIPVSKKVG-ELSLSQQQLVEIAKALTLDCRLLILDEPTAAL 169 Query: 185 NATEKLGLRELLVKIQAEGKTILLIEHDVKLMMGLCNRITVLDYGKPI 232 E L ++ +++ +G T++ I H + + LC IT+L G+ + Sbjct: 170 TEPEAQTLFSIVRQLRDQGMTVVYISHRMAEIFALCQHITILRDGRTV 217 Score = 65.5 bits (158), Expect = 2e-15 Identities = 59/237 (24%), Positives = 111/237 (46%), Gaps = 31/237 (13%) Query: 5 LLKIRDVS--KRFGGLQALNGVGITIERGQIYGLIGPNGAGKTTFFNVITGLYQPDTGTF 62 LL++R++S KRF + + + G+I G+ G GAG++ I L G+ Sbjct: 255 LLEVRNISDGKRF------HDIHFNLRPGEILGIGGLMGAGRSEIAQGICALQPLTRGSI 308 Query: 63 ELDGKP-----YSPSAPHEVAKAGIARTFQNIRLFGEMTVLENVMVGCHVRTKQNVFGAV 117 + G+P Y+ S + R ++ LF M + N+ +R + G Sbjct: 309 RIKGEPVRLKDYAASIQQRMVYLSEDR--KDAGLFLAMPIDWNISA-LDIRAVSH-HGLT 364 Query: 118 FRHKAAREEEAAIRE----KSQKLLDFVGIGQFAKRTARHLSYGDQRRLEIARALATDPQ 173 + R + A+ + K KL D V LS G+Q+++ +AR L+ P+ Sbjct: 365 LSPRRERLQAEALAQQVKLKRGKLSDPVS----------SLSGGNQQKVALARVLSVQPE 414 Query: 174 LLALDEPAAGMNATEKLGLRELLVKIQAEGKTILLIEHDVKLMMGLCNRITVLDYGK 230 ++ LDEP G++ + K + ++L + G +++I ++ ++GLC+RI V+ G+ Sbjct: 415 IVFLDEPTRGVDVSAKAEIYQILANLAGNGVGLVVISSELPELIGLCDRIIVIHEGR 471 Lambda K H 0.320 0.138 0.394 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 300 Number of extensions: 17 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 255 Length of database: 500 Length adjustment: 29 Effective length of query: 226 Effective length of database: 471 Effective search space: 106446 Effective search space used: 106446 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory